JAL-1821 patch for completeness - first model number is zero

[jalview.git] / src / jalview / ext / jmol / JalviewJmolBinding.java

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index cec9b0c..296892c 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -281,7 +281,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     String nSeconds = " ";
     if (files.length > 10)
     {
-      nSeconds = " 0.00001 ";
+      nSeconds = " 0.005 ";
     }
     else
     {
@@ -290,7 +290,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     }
     // see JAL-1345 - should really automatically turn off the animation for
     // large numbers of structures, but Jmol doesn't seem to allow that.
-    nSeconds = " ";
+    // nSeconds = " ";
     // union of all aligned positions are collected together.
     for (int a = 0; a < _alignment.length; a++)
     {
@@ -676,6 +676,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
           // applet path with docroot - discard as format won't match pdbfile
           mset[0] = m;
         }
+        _modelFileNameMap[0] = 0; // filename index for first model is always 0.
       }
       int j = 1;
       for (int i = 1; i < mset.length; i++)